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A Preliminary X-Ray Study of Murine Tnfaip8/Oxi-Α

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A Preliminary X-Ray Study of Murine Tnfaip8/Oxi-Α Int. J. Mol. Sci. 2014, 15, 4523-4530; doi:10.3390/ijms15034523 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Article A Preliminary X-ray Study of Murine Tnfaip8/Oxi-α Daeun Lee 1,†, Mi-Sun Kim 1,†, Jimin Park 1, Gil-Ja Jhon 2, Jin H. Son 1 and Dong Hae Shin 1,* 1 College of Pharmacy and Graduate School of Pharmaceutical Sciences, Global Top5 Research Program, Ewha Womans University, Seoul 120-750, Korea; E-Mails: [email protected] (D.L.); [email protected] (M.-S.K.); [email protected] (J.P.); [email protected] (J.H.S.) 2 Department of Chemistry and Nano Science, Global Top5 Research Program, Ewha Womans University, Seoul 120-750, Korea; E-Mail: [email protected] † These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +82-2-3277-4502; Fax: +82-2-3277-4918. Received: 28 January 2014; in revised form: 6 March 2014 / Accepted: 7 March 2014 / Published: 14 March 2014 Abstract: Tnfaip8/oxidative stress regulated gene-α (Oxi-α) is a novel protein expressed specifically in brain dopaminergic neurons and its over-expression has been reported to protect dopaminergic cells against OS-induced cell death. In this study, murine C165S mutant Tnfaip8/Oxi-α has been crystallized and X-ray data have been collected to 1.8 Å using synchrotron radiation. The crystal belonged to the primitive orthorhombic space group P21212, with unit-cell parameters a = 66.9, b = 72.3, c = 93.5 Å. A full structural determination is under way in order to provide insights into the structure-function relationships of this protein. Keywords: Parkinson’s disease; Oxi-α; oxidative stress; C165S mutant; X-ray crystallography 1. Introduction Parkinson’s disease (PD) is a degenerative disorder of the central nervous system. It is associated with a selective loss of the dopaminergic neurons in the midbrain area called substantia nigra pars compacta [1]. Since these neurons are essential for voluntary movements, their loss is associated with obvious symptoms such as tremor, rigidity, bradykinesia and postural instability. Oxidative stress (OS) Int. J. Mol. Sci. 2014, 15 4524 plays a significant pathogenic role in the progress of PD [2]. Tnfaip8/oxidative stress regulated gene-α (Oxi-α) is a novel protein expressed specifically in brain dopaminergic neurons and participates in OS-induced signaling [3]. The over-expression of Tnfaip8/Oxi-α has been reported to protect dopaminergic cells against OS-induced cell death. On the contrary, the Oxi-α gene knockdown affected dopaminergic neuronal susceptibility to OS. Oxi-α exerts this dopaminergic cell protective role by reducing autophagic cell death that is induced by OS [4]. Over-expression of Tnfaip8/Oxi-α dramatically inhibited the accumulation of autophagic vacuoles induced by autophagy inducers and OS. Intriguingly, the protective action of Tnfaip8/Oxi-α involves the activation of mTOR kinase which is a key member of the classical mTOR-dependent pathway of autophagy [4]. Increased levels of Tnfaip8/Oxi-α activate mTOR kinase regardless of the presence of rapamycin by increasing mTOR phosphorylation through an unknown mechanism. Although the precise mechanism by which Tnfaip8/Oxi-α activates mTOR kinase is not clear, Tnfaip8/Oxi-α is the first molecule to activate mTOR kinase and subsequently suppress the accumulation of autophagic vacuoles. In order to elucidate the structural and functional relationship of the Tnfaip8/Oxi-α family, we have initiated the determination of the three-dimensional structure of murine Tnfaip8/Oxi-α. There are four Tnfaip8/Oxi-α family members with ~54% sequence identity (Table 1). The crystal structure of Tnfaip8l2/Oxi-γ/TIPE2 has been published [5]. It belongs to all alpha proteins in SCOP [6] and shows a unique fold with a large hydrophobic central cavity. Tnfaip8l2 is essential for maintaining immune homeostasis [7] and plays a key role in a signal transduction pathway that links the inflammatory immune response to specific conditions after cerebral ischemia. Therefore, it is quite intriguing to elucidate common or unique structural properties of these families conferring diverse cellular functions. In this study, we report the cloning, overexpression, purification, crystallization and preliminary X-ray study of this enzyme. Table 1. Tnfaip8/Oxi-α family members. Family members Tnfaip8/Oxi-α Tnfaip8l1/Oxi-β Tnfaip8l2/Oxi-γ Tnfaip8l3/Oxi-δ Sequence identity 100% 54.4% 53.9% 54.4% with Tnfaip8/Oxi-α 2. Results and Discussion 2.1. Protein Expression and Purification The purification of native murine Tnfaip8/Oxi-α was not successful due to its heavy precipitation. Therefore, the C165S mutant was designed to avoid the precipitation induced presumably by non-specific disulfide bond formation. This strategy was successful and the mutant Tnfaip8/Oxi-α was well expressed and purified with the yield of 16.5 mg per liter of E. coli culture. After hydrophobic interaction chromatography, the mutant appeared to be approximately 99% pure, with a prominent protein band at around 24.3 kDa on SDS-PAGE (Figure 1). The minor protein band that moves faster than the major band on nonreducing SDS-PAGE was identified using nanoUPLC-ESI-q-TOF tandem MS (SYNAPT HDMS, Waters Co., Milford, MA, USA) with the previously published protocol [8]. It turned out to be a deletion version of the mutant Tnfaip8/Oxi-α not having N-terminal 36 amino acid Int. J. Mol. Sci. 2014, 15 4525 residues (data not shown). The same deletion was also observed in the native form even though the purification was done at 277 K. Figure 1. Coomassie-stained SDS-PAGE (12%) of C165S mutant Oxi-α. Lane 1, C165S mutant Oxi-α (1.1 mg); Lanes M, molecular-mass marker (labeled in kDa). 2.2. Protein Crystallization Although the protein solution was inhomogeneous, rice-shaped crystals of Tnfaip8/Oxi-α were obtained using ammonium sulfate as a precipitant (Figure 2A). It is noteworthy that 1.0 M ammonium sulfate was already included in the final concentrated protein solution. The improvement of crystal quality was achieved by addition of sodium citrate to the initial crystallization condition of 0.1 M sodium acetate pH 4.6, 1.0 M ammonium sulfate. Interestingly, the quality of crystals was gradually enhanced proportional to concentration of sodium citrate as described in the experimental section. Finally, high-quality crystals were obtained using a reservoir solution consisting of 0.1 M Bis-Tris propane pH 7.7, 1.2 M sodium citrate (Figure 2B). However, if ammonium sulfate was totally removed also from the concentrated protein solution, no crystal grew in the final crystallization condition. 2.3. X-ray Diffraction The best crystal grew to dimensions of 0.50 × 0.25 × 0.10 mm within a week at 296 K (Figure 2B). When the crystal was exposed to synchrotron radiation under cryogenic conditions, diffraction limit was 1.8 Å resolution. This crystal belongs to space P21212 and its Matthews coefficient [9] is 2.33 Å3·Da−1 when its asymmetric unit contains two Tnfaip8/Oxi-α protomers. These values are equivalent to solvent contents of 47.1%. The details of the data-collection statistics are presented in Table 2. Molecular replacement was performed by running PHASER [10] with the AutoMR wizard in PHENIX [11,12]. The crystal structure of Tnfaip8-like 2 (PDB entry 3f4m) was used as a search model. PHASER could place two protomers in the asymmetric with scores of RFZ (Rotation Function Z-score) = 13.4, TFZ (Translation Function Z-score) = 23.7 and LLG (Log Likelihood Gain) = 1489.0. Int. J. Mol. Sci. 2014, 15 4526 A relatively good electron density map was obtained and the initial model of mutant Tnfaip8/Oxi-α was well established with the PHENIX AutoBuild wizard [13] with R- (Residual Factor) and R-free factors of 0.25 and 0.27, respectively. Full structure determination is in progress. Figure 2. Crystals of C165S mutant Oxi-α. (A) Rice-shape crystals crystallized in 0.1 M sodium acetate pH 4.6, 1.0 M ammonium sulfate. The crystals grew to approximate dimensions of 0.10 × 0.10 × 0.02 mm in a week; (B) High-quality crystals crystallized in 0.1 M Bis-Tris propane pH 7.7, 1.2 M sodium citrate. These crystals grew to approximate dimensions of 0.50 × 0.25 × 0.10 mm in a week. (A) (B) Table 2. Data collection statistics for the mutant Oxi-α crystal. The values in parentheses are for the highest resolution shell. X-ray source Pohang Accelerator Laboratory (PAL) X-ray wavelength (Å) 0.97933 Temperature (K) 100 Space group P21212 Unit cell parameter -a (Å) 66.9 -b (Å) 72.3 -c (Å) 93.5 Volume fraction of solvent (%) 47.1 3 Vm (Å /Dalton) 2.33 Resolution range (Å) 50.0–1.8 (1.83–1.80) Total number of observed reflections 181684 Multiplicity 4.4 (4.5) Unique reflections 41052 (2090) † Rsym (%) 7.7 (46.1) Data completeness (%) 95.7 (99.1) Average I/σ (I) 16.4 (2.9) † Rsym = Σhkl Σi|Ihkl, i − Ihkl|/Σhkl Σi Ihkl, i, where Ihkl, i is the intensity of the ith observation of the unique reflection hkl and Ihkl is the mean of the intensities of all observations of reflection hkl. Int. J. Mol. Sci. 2014, 15 4527 3. Experimental Section 3.1. Expression and Purification of Tnfaip8/Oxi-α The cloning primers (Genotech, Daejeon, Korea) prepared for ligation-independent cloning (LIC) were 5'-GGCGGTGGTGGCGGCATGACCCTCATCGTTACCGGCG-3' for the forward strand and 5'-GTTCTTCTCCTTTGCGCCCCTACAGCTGGCCGAACAGCCAAC-3' for the reverse strand. The gene harboring murine Tnfaip8/Oxi-α (UniProt ID: Q921Z5) was amplified by PCR using 80 ng of the plasmid-cDNA [3] and 50 μM of primers with Deep Vent Polymerase (New England Biolabs, Inc., Beverly, MA, USA).
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